refactor: new image layout and organization (#13)

* refactor: rework how image are defined, in order to create others wrapper for others tools

* refactor: fix issues with ownership

* refactor: image share now information with others images type

* fix: update readme

README.md

@@ -144,7 +144,7 @@ Images are defined in the `cubbi/images/` directory, with each subdirectory cont
 - `Dockerfile`: Docker image definition
 - `entrypoint.sh`: Container entrypoint script
 - `cubbi-init.sh`: Standardized initialization script
-- `cubbi-image.yaml`: Image metadata and configuration
+- `cubbi_image.yaml`: Image metadata and configuration
 - `README.md`: Image documentation
 
 Cubbi automatically discovers and loads image definitions from the YAML files.

cubbi/cli.py

@@ -4,6 +4,9 @@ CLI for Cubbi Container Tool.
 
 import logging
 import os
+import shutil
+import tempfile
+from pathlib import Path
 from typing import List, Optional
 
 import typer
@@ -45,9 +48,7 @@ mcp_manager = MCPManager(config_manager=user_config)
 @app.callback()
 def main(
     ctx: typer.Context,
-    verbose: bool = typer.Option(
-        False, "--verbose", "-v", help="Enable verbose logging"
-    ),
+    verbose: bool = typer.Option(False, "--verbose", help="Enable verbose logging"),
 ) -> None:
     """Cubbi Container Tool
 
@@ -167,14 +168,12 @@ def create_session(
     gid: Optional[int] = typer.Option(
         None, "--gid", help="Group ID to run the container as (defaults to host user)"
     ),
-    model: Optional[str] = typer.Option(None, "--model", "-m", help="Model to use"),
+    model: Optional[str] = typer.Option(None, "--model", help="Model to use"),
     provider: Optional[str] = typer.Option(
         None, "--provider", "-p", help="Provider to use"
     ),
     ssh: bool = typer.Option(False, "--ssh", help="Start SSH server in the container"),
-    verbose: bool = typer.Option(
-        False, "--verbose", "-v", help="Enable verbose logging"
-    ),
+    verbose: bool = typer.Option(False, "--verbose", help="Enable verbose logging"),
 ) -> None:
     """Create a new Cubbi session
 
@@ -510,9 +509,60 @@ def build_image(
     # Build image name
     docker_image_name = f"monadical/cubbi-{image_name}:{tag}"
 
-    # Build the image
+    # Create temporary build directory
+    with tempfile.TemporaryDirectory() as temp_dir:
+        temp_path = Path(temp_dir)
+        console.print(f"Using temporary build directory: {temp_path}")
+
+        try:
+            # Copy all files from the image directory to temp directory
+            for item in image_path.iterdir():
+                if item.is_file():
+                    shutil.copy2(item, temp_path / item.name)
+                elif item.is_dir():
+                    shutil.copytree(item, temp_path / item.name)
+
+            # Copy shared cubbi_init.py to temp directory
+            shared_init_path = Path(__file__).parent / "images" / "cubbi_init.py"
+            if shared_init_path.exists():
+                shutil.copy2(shared_init_path, temp_path / "cubbi_init.py")
+                console.print("Copied shared cubbi_init.py to build context")
+            else:
+                console.print(
+                    f"[yellow]Warning: Shared cubbi_init.py not found at {shared_init_path}[/yellow]"
+                )
+
+            # Copy shared init-status.sh to temp directory
+            shared_status_path = Path(__file__).parent / "images" / "init-status.sh"
+            if shared_status_path.exists():
+                shutil.copy2(shared_status_path, temp_path / "init-status.sh")
+                console.print("Copied shared init-status.sh to build context")
+            else:
+                console.print(
+                    f"[yellow]Warning: Shared init-status.sh not found at {shared_status_path}[/yellow]"
+                )
+
+            # Copy image-specific plugin if it exists
+            plugin_path = image_path / f"{image_name.lower()}_plugin.py"
+            if plugin_path.exists():
+                shutil.copy2(plugin_path, temp_path / f"{image_name.lower()}_plugin.py")
+                console.print(f"Copied {image_name.lower()}_plugin.py to build context")
+
+            # Copy init-status.sh if it exists (for backward compatibility with shell connection)
+            init_status_path = image_path / "init-status.sh"
+            if init_status_path.exists():
+                shutil.copy2(init_status_path, temp_path / "init-status.sh")
+                console.print("Copied init-status.sh to build context")
+
+            # Build the image from temporary directory
             with console.status(f"Building image {docker_image_name}..."):
-        result = os.system(f"cd {image_path} && docker build -t {docker_image_name} .")
+                result = os.system(
+                    f"cd {temp_path} && docker build -t {docker_image_name} ."
+                )
+
+        except Exception as e:
+            console.print(f"[red]Error preparing build context: {e}[/red]")
+            return
 
     if result != 0:
         console.print("[red]Failed to build image[/red]")
@@ -1061,9 +1111,7 @@ def mcp_status(name: str = typer.Argument(..., help="MCP server name")) -> None:
 def start_mcp(
     name: Optional[str] = typer.Argument(None, help="MCP server name"),
     all_servers: bool = typer.Option(False, "--all", help="Start all MCP servers"),
-    verbose: bool = typer.Option(
-        False, "--verbose", "-v", help="Enable verbose logging"
-    ),
+    verbose: bool = typer.Option(False, "--verbose", help="Enable verbose logging"),
 ) -> None:
     """Start an MCP server or all servers"""
     # Set log level based on verbose flag

cubbi/config.py

@@ -108,7 +108,7 @@ class ConfigManager:
     def load_image_from_dir(self, image_dir: Path) -> Optional[Image]:
         """Load an image configuration from a directory"""
         # Check for image config file
-        yaml_path = image_dir / "cubbi-image.yaml"
+        yaml_path = image_dir / "cubbi_image.yaml"
         if not yaml_path.exists():
             return None
 
@@ -150,7 +150,7 @@ class ConfigManager:
         if not BUILTIN_IMAGES_DIR.exists():
             return images
 
-        # Search for cubbi-image.yaml files in each subdirectory
+        # Search for cubbi_image.yaml files in each subdirectory
         for image_dir in BUILTIN_IMAGES_DIR.iterdir():
             if image_dir.is_dir():
                 image = self.load_image_from_dir(image_dir)

cubbi/container.py

@@ -548,9 +548,6 @@ class ContainerManager:
 
                         # Connect the container to the network with session name as an alias
                         network.connect(container, aliases=[session_name])
-                        print(
-                            f"Connected to network: {network_name} with alias: {session_name}"
-                        )
                     except DockerException as e:
                         print(f"Error connecting to network {network_name}: {e}")
 
@@ -571,10 +568,13 @@ class ContainerManager:
                         print(
                             f"Connected session to MCP '{mcp_name}' via dedicated network: {dedicated_network_name}"
                         )
-                    except DockerException as e:
-                        print(
-                            f"Error connecting to MCP dedicated network '{dedicated_network_name}': {e}"
-                        )
+                    except DockerException:
+                        # print(
+                        #     f"Error connecting to MCP dedicated network '{dedicated_network_name}': {e}"
+                        # )
+                        # commented out, may be accessible through another attached network, it's
+                        # not mandatory here.
+                        pass
 
                 except Exception as e:
                     print(f"Error connecting session to MCP '{mcp_name}': {e}")
@@ -604,9 +604,6 @@ class ContainerManager:
 
                             # Connect the container to the network with session name as an alias
                             network.connect(container, aliases=[session_name])
-                            print(
-                                f"Connected to network: {network_name} with alias: {session_name}"
-                            )
                         except DockerException as e:
                             print(f"Error connecting to network {network_name}: {e}")
 

cubbi/images/__init__.py

@@ -1,3 +0,0 @@
-"""
-MAI container image management
-"""

cubbi/images/cubbi_init.py

@@ -0,0 +1,692 @@
+#!/usr/bin/env -S uv run --script
+# /// script
+# dependencies = ["ruamel.yaml"]
+# ///
+"""
+Standalone Cubbi initialization script
+
+This is a self-contained script that includes all the necessary initialization
+logic without requiring the full cubbi package to be installed.
+"""
+
+import grp
+import importlib.util
+import os
+import pwd
+import shutil
+import subprocess
+import sys
+from abc import ABC, abstractmethod
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import Any, Dict, List
+
+from ruamel.yaml import YAML
+
+
+# Status Management
+class StatusManager:
+    """Manages initialization status and logging"""
+
+    def __init__(
+        self, log_file: str = "/cubbi/init.log", status_file: str = "/cubbi/init.status"
+    ):
+        self.log_file = Path(log_file)
+        self.status_file = Path(status_file)
+        self._setup_logging()
+
+    def _setup_logging(self) -> None:
+        """Set up logging to both stdout and log file"""
+        self.log_file.touch(exist_ok=True)
+        self.set_status(False)
+
+    def log(self, message: str, level: str = "INFO") -> None:
+        """Log a message with timestamp"""
+        print(message)
+        sys.stdout.flush()
+
+        with open(self.log_file, "a") as f:
+            f.write(message + "\n")
+            f.flush()
+
+    def set_status(self, complete: bool) -> None:
+        """Set initialization completion status"""
+        status = "true" if complete else "false"
+        with open(self.status_file, "w") as f:
+            f.write(f"INIT_COMPLETE={status}\n")
+
+    def start_initialization(self) -> None:
+        """Mark initialization as started"""
+        self.set_status(False)
+
+    def complete_initialization(self) -> None:
+        """Mark initialization as completed"""
+        self.set_status(True)
+
+
+# Configuration Management
+@dataclass
+class PersistentConfig:
+    """Persistent configuration mapping"""
+
+    source: str
+    target: str
+    type: str = "directory"
+    description: str = ""
+
+
+@dataclass
+class ImageConfig:
+    """Cubbi image configuration"""
+
+    name: str
+    description: str
+    version: str
+    maintainer: str
+    image: str
+    persistent_configs: List[PersistentConfig] = field(default_factory=list)
+
+
+class ConfigParser:
+    """Parses Cubbi image configuration and environment variables"""
+
+    def __init__(self, config_file: str = "/cubbi/cubbi_image.yaml"):
+        self.config_file = Path(config_file)
+        self.environment: Dict[str, str] = dict(os.environ)
+
+    def load_image_config(self) -> ImageConfig:
+        """Load and parse the cubbi_image.yaml configuration"""
+        if not self.config_file.exists():
+            raise FileNotFoundError(f"Configuration file not found: {self.config_file}")
+
+        yaml = YAML(typ="safe")
+        with open(self.config_file, "r") as f:
+            config_data = yaml.load(f)
+
+        # Parse persistent configurations
+        persistent_configs = []
+        for pc_data in config_data.get("persistent_configs", []):
+            persistent_configs.append(PersistentConfig(**pc_data))
+
+        return ImageConfig(
+            name=config_data["name"],
+            description=config_data["description"],
+            version=config_data["version"],
+            maintainer=config_data["maintainer"],
+            image=config_data["image"],
+            persistent_configs=persistent_configs,
+        )
+
+    def get_cubbi_config(self) -> Dict[str, Any]:
+        """Get standard Cubbi configuration from environment"""
+        return {
+            "user_id": int(self.environment.get("CUBBI_USER_ID", "1000")),
+            "group_id": int(self.environment.get("CUBBI_GROUP_ID", "1000")),
+            "run_command": self.environment.get("CUBBI_RUN_COMMAND"),
+            "no_shell": self.environment.get("CUBBI_NO_SHELL", "false").lower()
+            == "true",
+            "config_dir": self.environment.get("CUBBI_CONFIG_DIR", "/cubbi-config"),
+            "persistent_links": self.environment.get("CUBBI_PERSISTENT_LINKS", ""),
+        }
+
+    def get_mcp_config(self) -> Dict[str, Any]:
+        """Get MCP server configuration from environment"""
+        mcp_count = int(self.environment.get("MCP_COUNT", "0"))
+        mcp_servers = []
+
+        for idx in range(mcp_count):
+            server = {
+                "name": self.environment.get(f"MCP_{idx}_NAME"),
+                "type": self.environment.get(f"MCP_{idx}_TYPE"),
+                "host": self.environment.get(f"MCP_{idx}_HOST"),
+                "url": self.environment.get(f"MCP_{idx}_URL"),
+            }
+            if server["name"]:  # Only add if name is present
+                mcp_servers.append(server)
+
+        return {"count": mcp_count, "servers": mcp_servers}
+
+
+# Core Management Classes
+class UserManager:
+    """Manages user and group creation/modification in containers"""
+
+    def __init__(self, status: StatusManager):
+        self.status = status
+        self.username = "cubbi"
+
+    def _run_command(self, cmd: list[str]) -> bool:
+        """Run a system command and log the result"""
+        try:
+            result = subprocess.run(cmd, capture_output=True, text=True, check=True)
+            if result.stdout:
+                self.status.log(f"Command output: {result.stdout.strip()}")
+            return True
+        except subprocess.CalledProcessError as e:
+            self.status.log(f"Command failed: {' '.join(cmd)}", "ERROR")
+            self.status.log(f"Error: {e.stderr}", "ERROR")
+            return False
+
+    def setup_user_and_group(self, user_id: int, group_id: int) -> bool:
+        """Set up user and group with specified IDs"""
+        self.status.log(
+            f"Setting up user '{self.username}' with UID: {user_id}, GID: {group_id}"
+        )
+
+        # Handle group creation/modification
+        try:
+            existing_group = grp.getgrnam(self.username)
+            if existing_group.gr_gid != group_id:
+                self.status.log(
+                    f"Modifying group '{self.username}' GID from {existing_group.gr_gid} to {group_id}"
+                )
+                if not self._run_command(
+                    ["groupmod", "-g", str(group_id), self.username]
+                ):
+                    return False
+        except KeyError:
+            if not self._run_command(["groupadd", "-g", str(group_id), self.username]):
+                return False
+
+        # Handle user creation/modification
+        try:
+            existing_user = pwd.getpwnam(self.username)
+            if existing_user.pw_uid != user_id or existing_user.pw_gid != group_id:
+                self.status.log(
+                    f"Modifying user '{self.username}' UID from {existing_user.pw_uid} to {user_id}, GID from {existing_user.pw_gid} to {group_id}"
+                )
+                if not self._run_command(
+                    [
+                        "usermod",
+                        "--uid",
+                        str(user_id),
+                        "--gid",
+                        str(group_id),
+                        self.username,
+                    ]
+                ):
+                    return False
+        except KeyError:
+            if not self._run_command(
+                [
+                    "useradd",
+                    "--shell",
+                    "/bin/bash",
+                    "--uid",
+                    str(user_id),
+                    "--gid",
+                    str(group_id),
+                    "--no-create-home",
+                    self.username,
+                ]
+            ):
+                return False
+
+        return True
+
+
+class DirectoryManager:
+    """Manages directory creation and permission setup"""
+
+    def __init__(self, status: StatusManager):
+        self.status = status
+
+    def create_directory(
+        self, path: str, user_id: int, group_id: int, mode: int = 0o755
+    ) -> bool:
+        """Create a directory with proper ownership and permissions"""
+        dir_path = Path(path)
+
+        try:
+            dir_path.mkdir(parents=True, exist_ok=True)
+            os.chown(path, user_id, group_id)
+            dir_path.chmod(mode)
+            self.status.log(f"Created directory: {path}")
+            return True
+        except Exception as e:
+            self.status.log(
+                f"Failed to create/configure directory {path}: {e}", "ERROR"
+            )
+            return False
+
+    def setup_standard_directories(self, user_id: int, group_id: int) -> bool:
+        """Set up standard Cubbi directories"""
+        directories = [
+            ("/app", 0o755),
+            ("/cubbi-config", 0o755),
+            ("/cubbi-config/home", 0o755),
+        ]
+
+        self.status.log("Setting up standard directories")
+
+        success = True
+        for dir_path, mode in directories:
+            if not self.create_directory(dir_path, user_id, group_id, mode):
+                success = False
+
+        # Create /home/cubbi as a symlink to /cubbi-config/home
+        try:
+            home_cubbi = Path("/home/cubbi")
+            if home_cubbi.exists() or home_cubbi.is_symlink():
+                home_cubbi.unlink()
+
+            self.status.log("Creating /home/cubbi as symlink to /cubbi-config/home")
+            home_cubbi.symlink_to("/cubbi-config/home")
+            os.lchown("/home/cubbi", user_id, group_id)
+        except Exception as e:
+            self.status.log(f"Failed to create home directory symlink: {e}", "ERROR")
+            success = False
+
+        # Create .local directory in the persistent home
+        local_dir = Path("/cubbi-config/home/.local")
+        if not self.create_directory(str(local_dir), user_id, group_id, 0o755):
+            success = False
+
+        # Copy /root/.local/bin to user's home if it exists
+        root_local_bin = Path("/root/.local/bin")
+        if root_local_bin.exists():
+            user_local_bin = Path("/cubbi-config/home/.local/bin")
+            try:
+                user_local_bin.mkdir(parents=True, exist_ok=True)
+
+                for item in root_local_bin.iterdir():
+                    if item.is_file():
+                        shutil.copy2(item, user_local_bin / item.name)
+                    elif item.is_dir():
+                        shutil.copytree(
+                            item, user_local_bin / item.name, dirs_exist_ok=True
+                        )
+
+                self._chown_recursive(user_local_bin, user_id, group_id)
+                self.status.log("Copied /root/.local/bin to user directory")
+
+            except Exception as e:
+                self.status.log(f"Failed to copy /root/.local/bin: {e}", "ERROR")
+                success = False
+
+        return success
+
+    def _chown_recursive(self, path: Path, user_id: int, group_id: int) -> None:
+        """Recursively change ownership of a directory"""
+        try:
+            os.chown(path, user_id, group_id)
+            for item in path.iterdir():
+                if item.is_dir():
+                    self._chown_recursive(item, user_id, group_id)
+                else:
+                    os.chown(item, user_id, group_id)
+        except Exception as e:
+            self.status.log(
+                f"Warning: Could not change ownership of {path}: {e}", "WARNING"
+            )
+
+
+class ConfigManager:
+    """Manages persistent configuration symlinks and mappings"""
+
+    def __init__(self, status: StatusManager):
+        self.status = status
+
+    def create_symlink(
+        self, source_path: str, target_path: str, user_id: int, group_id: int
+    ) -> bool:
+        """Create a symlink with proper ownership"""
+        try:
+            source = Path(source_path)
+
+            parent_dir = source.parent
+            if not parent_dir.exists():
+                self.status.log(f"Creating parent directory: {parent_dir}")
+                parent_dir.mkdir(parents=True, exist_ok=True)
+                os.chown(parent_dir, user_id, group_id)
+
+            self.status.log(f"Creating symlink: {source_path} -> {target_path}")
+            if source.is_symlink() or source.exists():
+                source.unlink()
+
+            source.symlink_to(target_path)
+            os.lchown(source_path, user_id, group_id)
+
+            return True
+        except Exception as e:
+            self.status.log(
+                f"Failed to create symlink {source_path} -> {target_path}: {e}", "ERROR"
+            )
+            return False
+
+    def _ensure_target_directory(
+        self, target_path: str, user_id: int, group_id: int
+    ) -> bool:
+        """Ensure the target directory exists with proper ownership"""
+        try:
+            target_dir = Path(target_path)
+            if not target_dir.exists():
+                self.status.log(f"Creating target directory: {target_path}")
+                target_dir.mkdir(parents=True, exist_ok=True)
+
+            # Set ownership of the target directory to cubbi user
+            os.chown(target_path, user_id, group_id)
+            self.status.log(f"Set ownership of {target_path} to {user_id}:{group_id}")
+            return True
+        except Exception as e:
+            self.status.log(
+                f"Failed to ensure target directory {target_path}: {e}", "ERROR"
+            )
+            return False
+
+    def setup_persistent_configs(
+        self, persistent_configs: List[PersistentConfig], user_id: int, group_id: int
+    ) -> bool:
+        """Set up persistent configuration symlinks from image config"""
+        if not persistent_configs:
+            self.status.log("No persistent configurations defined in image config")
+            return True
+
+        success = True
+        for config in persistent_configs:
+            # Ensure target directory exists with proper ownership
+            if not self._ensure_target_directory(config.target, user_id, group_id):
+                success = False
+                continue
+
+            if not self.create_symlink(config.source, config.target, user_id, group_id):
+                success = False
+
+        return success
+
+
+class CommandManager:
+    """Manages command execution and user switching"""
+
+    def __init__(self, status: StatusManager):
+        self.status = status
+        self.username = "cubbi"
+
+    def run_as_user(self, command: List[str], user: str = None) -> int:
+        """Run a command as the specified user using gosu"""
+        if user is None:
+            user = self.username
+
+        full_command = ["gosu", user] + command
+        self.status.log(f"Executing as {user}: {' '.join(command)}")
+
+        try:
+            result = subprocess.run(full_command, check=False)
+            return result.returncode
+        except Exception as e:
+            self.status.log(f"Failed to execute command: {e}", "ERROR")
+            return 1
+
+    def run_user_command(self, command: str) -> int:
+        """Run user-specified command as cubbi user"""
+        if not command:
+            return 0
+
+        self.status.log(f"Executing user command: {command}")
+        return self.run_as_user(["sh", "-c", command])
+
+    def exec_as_user(self, args: List[str]) -> None:
+        """Execute the final command as cubbi user (replaces current process)"""
+        if not args:
+            args = ["tail", "-f", "/dev/null"]
+
+        self.status.log(
+            f"Switching to user '{self.username}' and executing: {' '.join(args)}"
+        )
+
+        try:
+            os.execvp("gosu", ["gosu", self.username] + args)
+        except Exception as e:
+            self.status.log(f"Failed to exec as user: {e}", "ERROR")
+            sys.exit(1)
+
+
+# Tool Plugin System
+class ToolPlugin(ABC):
+    """Base class for tool-specific initialization plugins"""
+
+    def __init__(self, status: StatusManager, config: Dict[str, Any]):
+        self.status = status
+        self.config = config
+
+    @property
+    @abstractmethod
+    def tool_name(self) -> str:
+        """Return the name of the tool this plugin supports"""
+        pass
+
+    @abstractmethod
+    def initialize(self) -> bool:
+        """Main tool initialization logic"""
+        pass
+
+    def integrate_mcp_servers(self, mcp_config: Dict[str, Any]) -> bool:
+        """Integrate with available MCP servers"""
+        return True
+
+
+# Main Initializer
+class CubbiInitializer:
+    """Main Cubbi initialization orchestrator"""
+
+    def __init__(self):
+        self.status = StatusManager()
+        self.config_parser = ConfigParser()
+        self.user_manager = UserManager(self.status)
+        self.directory_manager = DirectoryManager(self.status)
+        self.config_manager = ConfigManager(self.status)
+        self.command_manager = CommandManager(self.status)
+
+    def run_initialization(self, final_args: List[str]) -> None:
+        """Run the complete initialization process"""
+        try:
+            self.status.start_initialization()
+
+            # Load configuration
+            image_config = self.config_parser.load_image_config()
+            cubbi_config = self.config_parser.get_cubbi_config()
+            mcp_config = self.config_parser.get_mcp_config()
+
+            self.status.log(f"Initializing {image_config.name} v{image_config.version}")
+
+            # Core initialization
+            success = self._run_core_initialization(image_config, cubbi_config)
+            if not success:
+                self.status.log("Core initialization failed", "ERROR")
+                sys.exit(1)
+
+            # Tool-specific initialization
+            success = self._run_tool_initialization(
+                image_config, cubbi_config, mcp_config
+            )
+            if not success:
+                self.status.log("Tool initialization failed", "ERROR")
+                sys.exit(1)
+
+            # Mark complete
+            self.status.complete_initialization()
+
+            # Handle commands
+            self._handle_command_execution(cubbi_config, final_args)
+
+        except Exception as e:
+            self.status.log(f"Initialization failed with error: {e}", "ERROR")
+            sys.exit(1)
+
+    def _run_core_initialization(self, image_config, cubbi_config) -> bool:
+        """Run core Cubbi initialization steps"""
+        user_id = cubbi_config["user_id"]
+        group_id = cubbi_config["group_id"]
+
+        if not self.user_manager.setup_user_and_group(user_id, group_id):
+            return False
+
+        if not self.directory_manager.setup_standard_directories(user_id, group_id):
+            return False
+
+        config_path = Path(cubbi_config["config_dir"])
+        if not config_path.exists():
+            self.status.log(f"Creating config directory: {cubbi_config['config_dir']}")
+            try:
+                config_path.mkdir(parents=True, exist_ok=True)
+                os.chown(cubbi_config["config_dir"], user_id, group_id)
+            except Exception as e:
+                self.status.log(f"Failed to create config directory: {e}", "ERROR")
+                return False
+
+        if not self.config_manager.setup_persistent_configs(
+            image_config.persistent_configs, user_id, group_id
+        ):
+            return False
+
+        return True
+
+    def _run_tool_initialization(self, image_config, cubbi_config, mcp_config) -> bool:
+        """Run tool-specific initialization"""
+        # Look for a tool-specific plugin file in the same directory
+        plugin_name = image_config.name.lower().replace("-", "_")
+        plugin_file = Path(__file__).parent / f"{plugin_name}_plugin.py"
+
+        if not plugin_file.exists():
+            self.status.log(
+                f"No tool-specific plugin found at {plugin_file}, skipping tool initialization"
+            )
+            return True
+
+        try:
+            # Dynamically load the plugin module
+            spec = importlib.util.spec_from_file_location(
+                f"{image_config.name.lower()}_plugin", plugin_file
+            )
+            plugin_module = importlib.util.module_from_spec(spec)
+            spec.loader.exec_module(plugin_module)
+
+            # Find the plugin class (should inherit from ToolPlugin)
+            plugin_class = None
+            for attr_name in dir(plugin_module):
+                attr = getattr(plugin_module, attr_name)
+                if (
+                    isinstance(attr, type)
+                    and hasattr(attr, "tool_name")
+                    and hasattr(attr, "initialize")
+                    and attr_name != "ToolPlugin"
+                ):  # Skip the base class
+                    plugin_class = attr
+                    break
+
+            if not plugin_class:
+                self.status.log(
+                    f"No valid plugin class found in {plugin_file}", "ERROR"
+                )
+                return False
+
+            # Instantiate and run the plugin
+            plugin = plugin_class(
+                self.status,
+                {
+                    "image_config": image_config,
+                    "cubbi_config": cubbi_config,
+                    "mcp_config": mcp_config,
+                },
+            )
+
+            self.status.log(f"Running {plugin.tool_name}-specific initialization")
+
+            if not plugin.initialize():
+                self.status.log(f"{plugin.tool_name} initialization failed", "ERROR")
+                return False
+
+            if not plugin.integrate_mcp_servers(mcp_config):
+                self.status.log(f"{plugin.tool_name} MCP integration failed", "ERROR")
+                return False
+
+            return True
+
+        except Exception as e:
+            self.status.log(
+                f"Failed to load or execute plugin {plugin_file}: {e}", "ERROR"
+            )
+            return False
+
+    def _handle_command_execution(self, cubbi_config, final_args):
+        """Handle command execution"""
+        exit_code = 0
+
+        if cubbi_config["run_command"]:
+            self.status.log("--- Executing initial command ---")
+            exit_code = self.command_manager.run_user_command(
+                cubbi_config["run_command"]
+            )
+            self.status.log(
+                f"--- Initial command finished (exit code: {exit_code}) ---"
+            )
+
+            if cubbi_config["no_shell"]:
+                self.status.log(
+                    "--- CUBBI_NO_SHELL=true, exiting container without starting shell ---"
+                )
+                sys.exit(exit_code)
+
+        self.command_manager.exec_as_user(final_args)
+
+
+def main() -> int:
+    """Main CLI entry point"""
+    import argparse
+
+    parser = argparse.ArgumentParser(
+        description="Cubbi container initialization script",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+This script initializes a Cubbi container environment by:
+1. Setting up user and group with proper IDs
+2. Creating standard directories with correct permissions
+3. Setting up persistent configuration symlinks
+4. Running tool-specific initialization if available
+5. Executing user commands or starting an interactive shell
+
+Environment Variables:
+  CUBBI_USER_ID      User ID for the cubbi user (default: 1000)
+  CUBBI_GROUP_ID     Group ID for the cubbi user (default: 1000)
+  CUBBI_RUN_COMMAND  Initial command to run before shell
+  CUBBI_NO_SHELL     Exit after run command instead of starting shell
+  CUBBI_CONFIG_DIR   Configuration directory path (default: /cubbi-config)
+  MCP_COUNT          Number of MCP servers to configure
+  MCP_<N>_NAME       Name of MCP server N
+  MCP_<N>_TYPE       Type of MCP server N
+  MCP_<N>_HOST       Host of MCP server N
+  MCP_<N>_URL        URL of MCP server N
+
+Examples:
+  cubbi_init.py                    # Initialize and start bash shell
+  cubbi_init.py --help             # Show this help message
+  cubbi_init.py /bin/zsh           # Initialize and start zsh shell
+  cubbi_init.py python script.py   # Initialize and run python script
+        """,
+    )
+
+    parser.add_argument(
+        "command",
+        nargs="*",
+        help="Command to execute after initialization (default: interactive shell)",
+    )
+
+    # Parse known args to handle cases where the command might have its own arguments
+    args, unknown = parser.parse_known_args()
+
+    # Combine parsed command with unknown args
+    final_args = args.command + unknown
+
+    # Handle the common case where docker CMD passes ["tail", "-f", "/dev/null"]
+    # This should be treated as "no specific command" (empty args)
+    if final_args == ["tail", "-f", "/dev/null"]:
+        final_args = []
+
+    initializer = CubbiInitializer()
+    initializer.run_initialization(final_args)
+
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

cubbi/images/goose/Dockerfile

@@ -7,8 +7,6 @@ LABEL description="Goose with MCP servers for Cubbi"
 RUN apt-get update && apt-get install -y --no-install-recommends \
     gosu \
     passwd \
-    git \
-    openssh-server \
     bash \
     curl \
     bzip2 \
@@ -17,13 +15,11 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libxcb1 \
     libdbus-1-3 \
     nano \
+    tmux \
+    git-core \
     vim \
     && rm -rf /var/lib/apt/lists/*
 
-# Set up SSH server directory (configuration will be handled by entrypoint if needed)
-RUN mkdir -p /var/run/sshd && chmod 0755 /var/run/sshd
-# Do NOT enable root login or set root password here
-
 # Install deps
 WORKDIR /tmp
 RUN curl -fsSL https://astral.sh/uv/install.sh -o install.sh && \
@@ -40,32 +36,24 @@ RUN curl -fsSL https://github.com/block/goose/releases/download/stable/download_
 # Create app directory
 WORKDIR /app
 
-# Copy initialization scripts
-COPY cubbi-init.sh /cubbi-init.sh
-COPY entrypoint.sh /entrypoint.sh
-COPY cubbi-image.yaml /cubbi-image.yaml
-COPY init-status.sh /init-status.sh
-COPY update-goose-config.py /usr/local/bin/update-goose-config.py
-
-# Extend env via bashrc
-
-# Make scripts executable
-RUN chmod +x /cubbi-init.sh /entrypoint.sh /init-status.sh \
-    /usr/local/bin/update-goose-config.py
-
-# Set up initialization status check on login
-RUN echo '[ -x /init-status.sh ] && /init-status.sh' >> /etc/bash.bashrc
+# Copy initialization system
+COPY cubbi_init.py /cubbi/cubbi_init.py
+COPY goose_plugin.py /cubbi/goose_plugin.py
+COPY cubbi_image.yaml /cubbi/cubbi_image.yaml
+COPY init-status.sh /cubbi/init-status.sh
+RUN chmod +x /cubbi/cubbi_init.py /cubbi/init-status.sh
+RUN echo '[ -x /cubbi/init-status.sh ] && /cubbi/init-status.sh' >> /etc/bash.bashrc
 
 # Set up environment
 ENV PYTHONUNBUFFERED=1
 ENV PYTHONDONTWRITEBYTECODE=1
+ENV UV_LINK_MODE=copy
+
+# Pre-install the cubbi_init
+RUN /cubbi/cubbi_init.py --help
+
 # Set WORKDIR to /app, common practice and expected by cubbi-init.sh
 WORKDIR /app
 
-# Expose ports
-EXPOSE 8000 22
-
-# Set entrypoint - container starts as root, entrypoint handles user switching
-ENTRYPOINT ["/entrypoint.sh"]
-# Default command if none is provided (entrypoint will run this via gosu)
+ENTRYPOINT ["/cubbi/cubbi_init.py"]
 CMD ["tail", "-f", "/dev/null"]

cubbi/images/goose/README.md

@@ -1,25 +1,50 @@
-# Goose Image for MC
+# Goose Image for Cubbi
 
 This image provides a containerized environment for running [Goose](https://goose.ai).
 
 ## Features
 
 - Pre-configured environment for Goose AI
-- Self-hosted instance integration
-- SSH access
-- Git repository integration
 - Langfuse logging support
 
 ## Environment Variables
 
+### Goose Configuration
+
+| Variable | Description | Required | Default |
+|----------|-------------|----------|---------|
+| `CUBBI_MODEL` | Model to use with Goose | No | - |
+| `CUBBI_PROVIDER` | Provider to use with Goose | No | - |
+
+### Langfuse Integration
+
+| Variable | Description | Required | Default |
+|----------|-------------|----------|---------|
+| `LANGFUSE_INIT_PROJECT_PUBLIC_KEY` | Langfuse public key | No | - |
+| `LANGFUSE_INIT_PROJECT_SECRET_KEY` | Langfuse secret key | No | - |
+| `LANGFUSE_URL` | Langfuse API URL | No | `https://cloud.langfuse.com` |
+
+### Cubbi Core Variables
+
+| Variable | Description | Required | Default |
+|----------|-------------|----------|---------|
+| `CUBBI_USER_ID` | UID for the container user | No | `1000` |
+| `CUBBI_GROUP_ID` | GID for the container user | No | `1000` |
+| `CUBBI_RUN_COMMAND` | Command to execute after initialization | No | - |
+| `CUBBI_NO_SHELL` | Exit after command execution | No | `false` |
+| `CUBBI_CONFIG_DIR` | Directory for persistent configurations | No | `/cubbi-config` |
+| `CUBBI_PERSISTENT_LINKS` | Semicolon-separated list of source:target symlinks | No | - |
+
+### MCP Integration Variables
+
 | Variable | Description | Required |
 |----------|-------------|----------|
-| `LANGFUSE_INIT_PROJECT_PUBLIC_KEY` | Langfuse public key | No |
-| `LANGFUSE_INIT_PROJECT_SECRET_KEY` | Langfuse secret key | No |
-| `LANGFUSE_URL` | Langfuse API URL | No |
-| `CUBBI_PROJECT_URL` | Project repository URL | No |
-| `CUBBI_GIT_SSH_KEY` | SSH key for Git authentication | No |
-| `CUBBI_GIT_TOKEN` | Token for Git authentication | No |
+| `MCP_COUNT` | Number of available MCP servers | No |
+| `MCP_NAMES` | JSON array of MCP server names | No |
+| `MCP_{idx}_NAME` | Name of MCP server at index | No |
+| `MCP_{idx}_TYPE` | Type of MCP server | No |
+| `MCP_{idx}_HOST` | Hostname of MCP server | No |
+| `MCP_{idx}_URL` | Full URL for remote MCP servers | No |
 
 ## Build
 
@@ -34,8 +59,5 @@ docker build -t monadical/cubbi-goose:latest .
 
 ```bash
 # Create a new session with this image
-cubbi session create --driver goose
-
-# Create with project repository
-cubbi  session create --driver goose --project github.com/username/repo
+cubbix -i goose
 ```

cubbi/images/goose/cubbi-init.sh

@@ -1,188 +0,0 @@
-#!/bin/bash
-# Standardized initialization script for Cubbi images
-
-# Redirect all output to both stdout and the log file
-exec > >(tee -a /init.log) 2>&1
-
-# Mark initialization as started
-echo "=== Cubbi Initialization started at $(date) ==="
-
-# --- START INSERTED BLOCK ---
-
-# Default UID/GID if not provided (should be passed by cubbi tool)
-CUBBI_USER_ID=${CUBBI_USER_ID:-1000}
-CUBBI_GROUP_ID=${CUBBI_GROUP_ID:-1000}
-
-echo "Using UID: $CUBBI_USER_ID, GID: $CUBBI_GROUP_ID"
-
-# Create group if it doesn't exist
-if ! getent group cubbi > /dev/null; then
-    groupadd -g $CUBBI_GROUP_ID cubbi
-else
-    # If group exists but has different GID, modify it
-    EXISTING_GID=$(getent group cubbi | cut -d: -f3)
-    if [ "$EXISTING_GID" != "$CUBBI_GROUP_ID" ]; then
-        groupmod -g $CUBBI_GROUP_ID cubbi
-    fi
-fi
-
-# Create user if it doesn't exist
-if ! getent passwd cubbi > /dev/null; then
-    useradd --shell /bin/bash --uid $CUBBI_USER_ID --gid $CUBBI_GROUP_ID --no-create-home cubbi
-else
-    # If user exists but has different UID/GID, modify it
-    EXISTING_UID=$(getent passwd cubbi | cut -d: -f3)
-    EXISTING_GID=$(getent passwd cubbi | cut -d: -f4)
-    if [ "$EXISTING_UID" != "$CUBBI_USER_ID" ] || [ "$EXISTING_GID" != "$CUBBI_GROUP_ID" ]; then
-        usermod --uid $CUBBI_USER_ID --gid $CUBBI_GROUP_ID cubbi
-    fi
-fi
-
-# Create home directory and set permissions
-mkdir -p /home/cubbi
-chown $CUBBI_USER_ID:$CUBBI_GROUP_ID /home/cubbi
-mkdir -p /app
-chown $CUBBI_USER_ID:$CUBBI_GROUP_ID /app
-
-# Copy /root/.local/bin to the user's home directory
-if [ -d /root/.local/bin ]; then
-    echo "Copying /root/.local/bin to /home/cubbi/.local/bin..."
-    mkdir -p /home/cubbi/.local/bin
-    cp -r /root/.local/bin/* /home/cubbi/.local/bin/
-    chown -R $CUBBI_USER_ID:$CUBBI_GROUP_ID /home/cubbi/.local
-fi
-
-# Start SSH server only if explicitly enabled
-if [ "$CUBBI_SSH_ENABLED" = "true" ]; then
-  echo "Starting SSH server..."
-  /usr/sbin/sshd
-else
-  echo "SSH server disabled (use --ssh flag to enable)"
-fi
-
-# --- END INSERTED BLOCK ---
-
-echo "INIT_COMPLETE=false" > /init.status
-
-# Project initialization
-if [ -n "$CUBBI_PROJECT_URL" ]; then
-    echo "Initializing project: $CUBBI_PROJECT_URL"
-
-    # Set up SSH key if provided
-    if [ -n "$CUBBI_GIT_SSH_KEY" ]; then
-        mkdir -p ~/.ssh
-        echo "$CUBBI_GIT_SSH_KEY" > ~/.ssh/id_ed25519
-        chmod 600 ~/.ssh/id_ed25519
-        ssh-keyscan github.com >> ~/.ssh/known_hosts 2>/dev/null
-        ssh-keyscan gitlab.com >> ~/.ssh/known_hosts 2>/dev/null
-        ssh-keyscan bitbucket.org >> ~/.ssh/known_hosts 2>/dev/null
-    fi
-
-    # Set up token if provided
-    if [ -n "$CUBBI_GIT_TOKEN" ]; then
-        git config --global credential.helper store
-        echo "https://$CUBBI_GIT_TOKEN:x-oauth-basic@github.com" > ~/.git-credentials
-    fi
-
-    # Clone repository
-    git clone $CUBBI_PROJECT_URL /app
-    cd /app
-
-    # Run project-specific initialization if present
-    if [ -f "/app/.cubbi/init.sh" ]; then
-        bash /app/.cubbi/init.sh
-    fi
-
-    # Persistent configs are now directly mounted as volumes
-    # No need to create symlinks anymore
-    if [ -n "$CUBBI_CONFIG_DIR" ] && [ -d "$CUBBI_CONFIG_DIR" ]; then
-        echo "Using persistent configuration volumes (direct mounts)"
-    fi
-fi
-
-# Goose uses self-hosted instance, no API key required
-
-# Set up Langfuse logging if credentials are provided
-if [ -n "$LANGFUSE_INIT_PROJECT_SECRET_KEY" ] && [ -n "$LANGFUSE_INIT_PROJECT_PUBLIC_KEY" ]; then
-    echo "Setting up Langfuse logging"
-    export LANGFUSE_INIT_PROJECT_SECRET_KEY="$LANGFUSE_INIT_PROJECT_SECRET_KEY"
-    export LANGFUSE_INIT_PROJECT_PUBLIC_KEY="$LANGFUSE_INIT_PROJECT_PUBLIC_KEY"
-    export LANGFUSE_URL="${LANGFUSE_URL:-https://cloud.langfuse.com}"
-fi
-
-# Ensure /cubbi-config directory exists (required for symlinks)
-if [ ! -d "/cubbi-config" ]; then
-    echo "Creating /cubbi-config directory since it doesn't exist"
-    mkdir -p /cubbi-config
-    chown $CUBBI_USER_ID:$CUBBI_GROUP_ID /cubbi-config
-fi
-
-# Create symlinks for persistent configurations defined in the image
-if [ -n "$CUBBI_PERSISTENT_LINKS" ]; then
-    echo "Creating persistent configuration symlinks..."
-    # Split by semicolon
-    IFS=';' read -ra LINKS <<< "$CUBBI_PERSISTENT_LINKS"
-    for link_pair in "${LINKS[@]}"; do
-        # Split by colon
-        IFS=':' read -r source_path target_path <<< "$link_pair"
-
-        if [ -z "$source_path" ] || [ -z "$target_path" ]; then
-            echo "Warning: Invalid link pair format '$link_pair', skipping."
-            continue
-        fi
-
-        echo "Processing link: $source_path -> $target_path"
-        parent_dir=$(dirname "$source_path")
-
-        # Ensure parent directory of the link source exists and is owned by cubbi
-        if [ ! -d "$parent_dir" ]; then
-             echo "Creating parent directory: $parent_dir"
-             mkdir -p "$parent_dir"
-             echo "Changing ownership of parent $parent_dir to $CUBBI_USER_ID:$CUBBI_GROUP_ID"
-             chown "$CUBBI_USER_ID:$CUBBI_GROUP_ID" "$parent_dir" || echo "Warning: Could not chown parent $parent_dir"
-        fi
-
-        # Create the symlink (force, no-dereference)
-        echo "Creating symlink: ln -sfn $target_path $source_path"
-        ln -sfn "$target_path" "$source_path"
-        # Optionally, change ownership of the symlink itself
-        echo "Changing ownership of symlink $source_path to $CUBBI_USER_ID:$CUBBI_GROUP_ID"
-        chown -h "$CUBBI_USER_ID:$CUBBI_GROUP_ID" "$source_path" || echo "Warning: Could not chown symlink $source_path"
-
-    done
-    echo "Persistent configuration symlinks created."
-fi
-
-# Update Goose configuration with available MCP servers (run as cubbi after symlinks are created)
-if [ -f "/usr/local/bin/update-goose-config.py" ]; then
-    echo "Updating Goose configuration with MCP servers as cubbi..."
-    gosu cubbi /usr/local/bin/update-goose-config.py
-elif [ -f "$(dirname "$0")/update-goose-config.py" ]; then
-    echo "Updating Goose configuration with MCP servers as cubbi..."
-    gosu cubbi "$(dirname "$0")/update-goose-config.py"
-else
-    echo "Warning: update-goose-config.py script not found. Goose configuration will not be updated."
-fi
-
-# Run the user command first, if set, as cubbi
-if [ -n "$CUBBI_RUN_COMMAND" ]; then
-    echo "--- Executing initial command: $CUBBI_RUN_COMMAND ---";
-    gosu cubbi sh -c "$CUBBI_RUN_COMMAND"; # Run user command as cubbi
-    COMMAND_EXIT_CODE=$?;
-    echo "--- Initial command finished (exit code: $COMMAND_EXIT_CODE) ---";
-
-    # If CUBBI_NO_SHELL is set, exit instead of starting a shell
-    if [ "$CUBBI_NO_SHELL" = "true" ]; then
-        echo "--- CUBBI_NO_SHELL=true, exiting container without starting shell ---";
-        # Mark initialization as complete before exiting
-        echo "=== Cubbi Initialization completed at $(date) ==="
-        echo "INIT_COMPLETE=true" > /init.status
-        exit $COMMAND_EXIT_CODE;
-    fi;
-fi;
-
-# Mark initialization as complete
-echo "=== Cubbi Initialization completed at $(date) ==="
-echo "INIT_COMPLETE=true" > /init.status
-
-exec gosu cubbi "$@"

cubbi/images/goose/cubbi_image.yaml

@@ -24,29 +24,8 @@ environment:
     required: false
     default: https://cloud.langfuse.com
 
-  # Project environment variables
-  - name: CUBBI_PROJECT_URL
-    description: Project repository URL
-    required: false
-
-  - name: CUBBI_PROJECT_TYPE
-    description: Project repository type (git, svn, etc.)
-    required: false
-    default: git
-
-  - name: CUBBI_GIT_SSH_KEY
-    description: SSH key for Git authentication
-    required: false
-    sensitive: true
-
-  - name: CUBBI_GIT_TOKEN
-    description: Token for Git authentication
-    required: false
-    sensitive: true
-
 ports:
-  - 8000 # Main application
-  - 22 # SSH server
+  - 8000
 
 volumes:
   - mountPath: /app
@@ -57,7 +36,3 @@ persistent_configs:
     target: "/cubbi-config/goose-app"
     type: "directory"
     description: "Goose memory"
-  - source: "/home/cubbi/.config/goose"
-    target: "/cubbi-config/goose-config"
-    type: "directory"
-    description: "Goose configuration"

cubbi/images/goose/entrypoint.sh

@@ -1,7 +0,0 @@
-#!/bin/bash
-# Entrypoint script for Goose image
-# Executes the standard initialization script, which handles user setup,
-# service startup (like sshd), and switching to the non-root user
-# before running the container's command (CMD).
-
-exec /cubbi-init.sh "$@"

cubbi/images/goose/goose_plugin.py

@@ -0,0 +1,195 @@
+#!/usr/bin/env python3
+"""
+Goose-specific plugin for Cubbi initialization
+"""
+
+import os
+from pathlib import Path
+from typing import Any, Dict
+
+from cubbi_init import ToolPlugin
+from ruamel.yaml import YAML
+
+
+class GoosePlugin(ToolPlugin):
+    """Plugin for Goose AI tool initialization"""
+
+    @property
+    def tool_name(self) -> str:
+        return "goose"
+
+    def _get_user_ids(self) -> tuple[int, int]:
+        """Get the cubbi user and group IDs from environment"""
+        user_id = int(os.environ.get("CUBBI_USER_ID", "1000"))
+        group_id = int(os.environ.get("CUBBI_GROUP_ID", "1000"))
+        return user_id, group_id
+
+    def _set_ownership(self, path: Path) -> None:
+        """Set ownership of a path to the cubbi user"""
+        user_id, group_id = self._get_user_ids()
+        try:
+            os.chown(path, user_id, group_id)
+        except OSError as e:
+            self.status.log(f"Failed to set ownership for {path}: {e}", "WARNING")
+
+    def _get_user_config_path(self) -> Path:
+        """Get the correct config path for the cubbi user"""
+        return Path("/home/cubbi/.config/goose")
+
+    def _ensure_user_config_dir(self) -> Path:
+        """Ensure config directory exists with correct ownership"""
+        config_dir = self._get_user_config_path()
+
+        # Create the full directory path
+        try:
+            config_dir.mkdir(parents=True, exist_ok=True)
+        except FileExistsError:
+            # Directory already exists, which is fine
+            pass
+        except OSError as e:
+            self.status.log(
+                f"Failed to create config directory {config_dir}: {e}", "ERROR"
+            )
+            return config_dir
+
+        # Set ownership for the directories
+        config_parent = config_dir.parent
+        if config_parent.exists():
+            self._set_ownership(config_parent)
+
+        if config_dir.exists():
+            self._set_ownership(config_dir)
+
+        return config_dir
+
+    def initialize(self) -> bool:
+        """Initialize Goose configuration"""
+        self._ensure_user_config_dir()
+        return self.setup_tool_configuration()
+
+    def setup_tool_configuration(self) -> bool:
+        """Set up Goose configuration file"""
+        # Ensure directory exists before writing
+        config_dir = self._ensure_user_config_dir()
+        if not config_dir.exists():
+            self.status.log(
+                f"Config directory {config_dir} does not exist and could not be created",
+                "ERROR",
+            )
+            return False
+
+        config_file = config_dir / "config.yaml"
+        yaml = YAML(typ="safe")
+
+        # Load or initialize configuration
+        if config_file.exists():
+            with config_file.open("r") as f:
+                config_data = yaml.load(f) or {}
+        else:
+            config_data = {}
+
+        if "extensions" not in config_data:
+            config_data["extensions"] = {}
+
+        # Add default developer extension
+        config_data["extensions"]["developer"] = {
+            "enabled": True,
+            "name": "developer",
+            "timeout": 300,
+            "type": "builtin",
+        }
+
+        # Update with environment variables
+        goose_model = os.environ.get("CUBBI_MODEL")
+        goose_provider = os.environ.get("CUBBI_PROVIDER")
+
+        if goose_model:
+            config_data["GOOSE_MODEL"] = goose_model
+            self.status.log(f"Set GOOSE_MODEL to {goose_model}")
+
+        if goose_provider:
+            config_data["GOOSE_PROVIDER"] = goose_provider
+            self.status.log(f"Set GOOSE_PROVIDER to {goose_provider}")
+
+        try:
+            with config_file.open("w") as f:
+                yaml.dump(config_data, f)
+
+            # Set ownership of the config file to cubbi user
+            self._set_ownership(config_file)
+
+            self.status.log(f"Updated Goose configuration at {config_file}")
+            return True
+        except Exception as e:
+            self.status.log(f"Failed to write Goose configuration: {e}", "ERROR")
+            return False
+
+    def integrate_mcp_servers(self, mcp_config: Dict[str, Any]) -> bool:
+        """Integrate Goose with available MCP servers"""
+        if mcp_config["count"] == 0:
+            self.status.log("No MCP servers to integrate")
+            return True
+
+        # Ensure directory exists before writing
+        config_dir = self._ensure_user_config_dir()
+        if not config_dir.exists():
+            self.status.log(
+                f"Config directory {config_dir} does not exist and could not be created",
+                "ERROR",
+            )
+            return False
+
+        config_file = config_dir / "config.yaml"
+        yaml = YAML(typ="safe")
+
+        if config_file.exists():
+            with config_file.open("r") as f:
+                config_data = yaml.load(f) or {}
+        else:
+            config_data = {"extensions": {}}
+
+        if "extensions" not in config_data:
+            config_data["extensions"] = {}
+
+        for server in mcp_config["servers"]:
+            server_name = server["name"]
+            server_host = server["host"]
+            server_url = server["url"]
+
+            if server_name and server_host:
+                mcp_url = f"http://{server_host}:8080/sse"
+                self.status.log(f"Adding MCP extension: {server_name} - {mcp_url}")
+
+                config_data["extensions"][server_name] = {
+                    "enabled": True,
+                    "name": server_name,
+                    "timeout": 60,
+                    "type": "sse",
+                    "uri": mcp_url,
+                    "envs": {},
+                }
+            elif server_name and server_url:
+                self.status.log(
+                    f"Adding remote MCP extension: {server_name} - {server_url}"
+                )
+
+                config_data["extensions"][server_name] = {
+                    "enabled": True,
+                    "name": server_name,
+                    "timeout": 60,
+                    "type": "sse",
+                    "uri": server_url,
+                    "envs": {},
+                }
+
+        try:
+            with config_file.open("w") as f:
+                yaml.dump(config_data, f)
+
+            # Set ownership of the config file to cubbi user
+            self._set_ownership(config_file)
+
+            return True
+        except Exception as e:
+            self.status.log(f"Failed to integrate MCP servers: {e}", "ERROR")
+            return False

cubbi/images/goose/update-goose-config.py

@@ -1,106 +0,0 @@
-#!/usr/bin/env -S uv run --script
-# /// script
-# dependencies = ["ruamel.yaml"]
-# ///
-import json
-import os
-from pathlib import Path
-
-from ruamel.yaml import YAML
-
-# Path to goose config
-GOOSE_CONFIG = Path.home() / ".config/goose/config.yaml"
-CONFIG_DIR = GOOSE_CONFIG.parent
-
-# Create config directory if it doesn't exist
-CONFIG_DIR.mkdir(parents=True, exist_ok=True)
-
-
-def update_config():
-    """Update Goose configuration based on environment variables and config file"""
-
-    yaml = YAML()
-
-    # Load or initialize the YAML configuration
-    if not GOOSE_CONFIG.exists():
-        config_data = {"extensions": {}}
-    else:
-        with GOOSE_CONFIG.open("r") as f:
-            config_data = yaml.load(f)
-            if "extensions" not in config_data:
-                config_data["extensions"] = {}
-
-    # Add default developer extension
-    config_data["extensions"]["developer"] = {
-        "enabled": True,
-        "name": "developer",
-        "timeout": 300,
-        "type": "builtin",
-    }
-
-    # Update goose configuration with model and provider from environment variables
-    goose_model = os.environ.get("CUBBI_MODEL")
-    goose_provider = os.environ.get("CUBBI_PROVIDER")
-
-    if goose_model:
-        config_data["GOOSE_MODEL"] = goose_model
-        print(f"Set GOOSE_MODEL to {goose_model}")
-
-    if goose_provider:
-        config_data["GOOSE_PROVIDER"] = goose_provider
-        print(f"Set GOOSE_PROVIDER to {goose_provider}")
-
-    # Get MCP information from environment variables
-    mcp_count = int(os.environ.get("MCP_COUNT", "0"))
-    mcp_names_str = os.environ.get("MCP_NAMES", "[]")
-
-    try:
-        mcp_names = json.loads(mcp_names_str)
-        print(f"Found {mcp_count} MCP servers: {', '.join(mcp_names)}")
-    except json.JSONDecodeError:
-        mcp_names = []
-        print("Error parsing MCP_NAMES environment variable")
-
-    # Process each MCP - collect the MCP configs to add or update
-    for idx in range(mcp_count):
-        mcp_name = os.environ.get(f"MCP_{idx}_NAME")
-        mcp_type = os.environ.get(f"MCP_{idx}_TYPE")
-        mcp_host = os.environ.get(f"MCP_{idx}_HOST")
-
-        # Always use container's SSE port (8080) not the host-bound port
-        if mcp_name and mcp_host:
-            # Use standard MCP SSE port (8080)
-            mcp_url = f"http://{mcp_host}:8080/sse"
-            print(f"Processing MCP extension: {mcp_name} ({mcp_type}) - {mcp_url}")
-            config_data["extensions"][mcp_name] = {
-                "enabled": True,
-                "name": mcp_name,
-                "timeout": 60,
-                "type": "sse",
-                "uri": mcp_url,
-                "envs": {},
-            }
-        elif mcp_name and os.environ.get(f"MCP_{idx}_URL"):
-            # For remote MCPs, use the URL provided in environment
-            mcp_url = os.environ.get(f"MCP_{idx}_URL")
-            print(
-                f"Processing remote MCP extension: {mcp_name} ({mcp_type}) - {mcp_url}"
-            )
-            config_data["extensions"][mcp_name] = {
-                "enabled": True,
-                "name": mcp_name,
-                "timeout": 60,
-                "type": "sse",
-                "uri": mcp_url,
-                "envs": {},
-            }
-
-    # Write the updated configuration back to the file
-    with GOOSE_CONFIG.open("w") as f:
-        yaml.dump(config_data, f)
-
-    print(f"Updated Goose configuration at {GOOSE_CONFIG}")
-
-
-if __name__ == "__main__":
-    update_config()

cubbi/images/init-status.sh

@@ -6,17 +6,20 @@ if [ "$(id -u)" != "0" ]; then
     exit 0
 fi
 
+# Ensure files exist before checking them
+touch /cubbi/init.status /cubbi/init.log
+
 # Quick check instead of full logic
-if ! grep -q "INIT_COMPLETE=true" "/init.status" 2>/dev/null; then
+if ! grep -q "INIT_COMPLETE=true" "/cubbi/init.status" 2>/dev/null; then
     # Only follow logs if initialization is incomplete
-    if [ -f "/init.log" ]; then
+    if [ -f "/cubbi/init.log" ]; then
         echo "----------------------------------------"
-        tail -f /init.log &
+        tail -f /cubbi/init.log &
         tail_pid=$!
 
         # Check every second if initialization has completed
         while true; do
-            if grep -q "INIT_COMPLETE=true" "/init.status" 2>/dev/null; then
+            if grep -q "INIT_COMPLETE=true" "/cubbi/init.status" 2>/dev/null; then
                 kill $tail_pid 2>/dev/null
                 echo "----------------------------------------"
                 break
@@ -28,4 +31,4 @@ if ! grep -q "INIT_COMPLETE=true" "/init.status" 2>/dev/null; then
     fi
 fi
 
-exec gosu cubbi /bin/bash -il
+exec gosu cubbi /bin/bash -i

docs/specs/1_SPECIFICATIONS.md

@@ -387,7 +387,7 @@ Cubbi provides persistent storage for project-specific configurations that need
 
 2. **Image Configuration**:
    - Each image can specify configuration files/directories that should persist across sessions
-   - These are defined in the image's `cubbi-image.yaml` file in the `persistent_configs` section
+   - These are defined in the image's `cubbi_image.yaml` file in the `persistent_configs` section
    - Example for Goose image:
      ```yaml
      persistent_configs:
@@ -458,7 +458,7 @@ Each image is a Docker container with a standardized structure:
 /
 ├── entrypoint.sh      # Container initialization
 ├── cubbi-init.sh      # Standardized initialization script
-├── cubbi-image.yaml   # Image metadata and configuration
+├── cubbi_image.yaml   # Image metadata and configuration
 ├── tool/              # AI tool installation
 └── ssh/               # SSH server configuration
 ```
@@ -500,7 +500,7 @@ fi
 # Image-specific initialization continues...
 ```
 
-### Image Configuration (cubbi-image.yaml)
+### Image Configuration (cubbi_image.yaml)
 
 ```yaml
 name: goose

docs/specs/3_IMAGE.md

@@ -0,0 +1,327 @@
+# Cubbi Image Specifications
+
+## Overview
+
+This document defines the specifications and requirements for building Cubbi-compatible container images. These images serve as isolated development environments for AI tools within the Cubbi platform.
+
+## Architecture
+
+Cubbi images use a Python-based initialization system with a plugin architecture that separates core Cubbi functionality from tool-specific configuration.
+
+### Core Components
+
+1. **Image Metadata File** (`cubbi_image.yaml`) - *Tool-specific*
+2. **Container Definition** (`Dockerfile`) - *Tool-specific*
+3. **Python Initialization Script** (`cubbi_init.py`) - *Shared across all images*
+4. **Tool-specific Plugins** (e.g., `goose_plugin.py`) - *Tool-specific*
+5. **Status Tracking Scripts** (`init-status.sh`) - *Shared across all images*
+
+## Image Metadata Specification
+
+### Required Fields
+
+```yaml
+name: string               # Unique identifier for the image
+description: string        # Human-readable description
+version: string           # Semantic version (e.g., "1.0.0")
+maintainer: string        # Contact information
+image: string             # Docker image name and tag
+```
+
+### Environment Variables
+
+```yaml
+environment:
+  - name: string          # Variable name
+    description: string   # Human-readable description
+    required: boolean     # Whether variable is mandatory
+    sensitive: boolean    # Whether variable contains secrets
+    default: string       # Default value (optional)
+```
+
+#### Standard Environment Variables
+
+All images MUST support these standard environment variables:
+
+- `CUBBI_USER_ID`: UID for the container user (default: 1000)
+- `CUBBI_GROUP_ID`: GID for the container user (default: 1000)
+- `CUBBI_RUN_COMMAND`: Command to execute after initialization
+- `CUBBI_NO_SHELL`: Exit after command execution ("true"/"false")
+- `CUBBI_CONFIG_DIR`: Directory for persistent configurations (default: "/cubbi-config")
+- `CUBBI_MODEL`: Model to use for the tool
+- `CUBBI_PROVIDER`: Provider to use for the tool
+
+#### MCP Integration Variables
+
+For MCP (Model Context Protocol) integration:
+
+- `MCP_COUNT`: Number of available MCP servers
+- `MCP_{idx}_NAME`: Name of MCP server at index
+- `MCP_{idx}_TYPE`: Type of MCP server
+- `MCP_{idx}_HOST`: Hostname of MCP server
+- `MCP_{idx}_URL`: Full URL for remote MCP servers
+
+### Network Configuration
+
+```yaml
+ports:
+  - number              # Port to expose (e.g., 8000)
+```
+
+### Storage Configuration
+
+```yaml
+volumes:
+  - mountPath: string   # Path inside container
+    description: string # Purpose of the volume
+
+persistent_configs:
+  - source: string      # Path inside container
+    target: string      # Path in persistent storage
+    type: string        # "file" or "directory"
+    description: string # Purpose of the configuration
+```
+
+## Container Requirements
+
+### Base System Dependencies
+
+All images MUST include:
+
+- `python3` - For the initialization system
+- `gosu` - For secure user switching
+- `bash` - For script execution
+
+### Python Dependencies
+
+The Cubbi initialization system requires:
+
+- `ruamel.yaml` - For YAML configuration parsing
+
+### User Management
+
+Images MUST:
+
+1. Run as root initially for setup
+2. Create a non-root user (`cubbi`) with configurable UID/GID
+3. Switch to the non-root user for tool execution
+4. Handle user ID mapping for volume permissions
+
+### Directory Structure
+
+Standard directories:
+
+- `/app` - Primary working directory (owned by cubbi user)
+- `/home/cubbi` - User home directory
+- `/cubbi-config` - Persistent configuration storage
+- `/cubbi/init.log` - Initialization log file
+- `/cubbi/init.status` - Initialization status tracking
+- `/cubbi/cubbi_image.yaml` - Image configuration
+
+## Initialization System
+
+### Shared Scripts
+
+The following scripts are **shared across all Cubbi images** and should be copied from the main Cubbi repository:
+
+#### Main Script (`cubbi_init.py`) - *Shared*
+
+The standalone initialization script that:
+
+1. Sets up user and group with proper IDs
+2. Creates standard directories with correct permissions
+3. Sets up persistent configuration symlinks
+4. Runs tool-specific initialization
+5. Executes user commands or starts interactive shell
+
+The script supports:
+- `--help` for usage information
+- Argument passing to final command
+- Environment variable configuration
+- Plugin-based tool initialization
+
+#### Status Tracking Script (`init-status.sh`) - *Shared*
+
+A bash script that:
+- Monitors initialization progress
+- Displays logs during setup
+- Ensures files exist before operations
+- Switches to user shell when complete
+
+### Tool-Specific Components
+
+#### Tool Plugins (`{tool}_plugin.py`) - *Tool-specific*
+
+Each tool MUST provide a plugin (`{tool}_plugin.py`) implementing:
+
+```python
+from cubbi_init import ToolPlugin
+
+class MyToolPlugin(ToolPlugin):
+    @property
+    def tool_name(self) -> str:
+        return "mytool"
+
+    def initialize(self) -> bool:
+        """Main tool initialization logic"""
+        # Tool-specific setup
+        return True
+
+    def integrate_mcp_servers(self, mcp_config: Dict[str, Any]) -> bool:
+        """Integrate with available MCP servers"""
+        # MCP integration logic
+        return True
+```
+
+#### Image Configuration (`cubbi_image.yaml`) - *Tool-specific*
+
+Each tool provides its own metadata file defining:
+- Tool-specific environment variables
+- Port configurations
+- Volume mounts
+- Persistent configuration mappings
+
+## Plugin Architecture
+
+### Plugin Discovery
+
+Plugins are automatically discovered by:
+
+1. Looking for `{image_name}_plugin.py` in the same directory as `cubbi_init.py`
+2. Loading classes that inherit from `ToolPlugin`
+3. Executing initialization and MCP integration
+
+### Plugin Requirements
+
+Tool plugins MUST:
+- Inherit from `ToolPlugin` base class
+- Implement `tool_name` property
+- Implement `initialize()` method
+- Optionally implement `integrate_mcp_servers()` method
+- Use ruamel.yaml for configuration file operations
+
+## Security Requirements
+
+### User Isolation
+
+- Container MUST NOT run processes as root after initialization
+- All user processes MUST run as the `cubbi` user
+- Proper file ownership and permissions MUST be maintained
+
+### Secrets Management
+
+- Sensitive environment variables MUST be marked as `sensitive: true`
+- SSH keys and tokens MUST have restricted permissions (600)
+- No secrets SHOULD be logged or exposed in configuration files
+
+### Network Security
+
+- Only necessary ports SHOULD be exposed
+- Network services should be properly configured and secured
+
+## Integration Requirements
+
+### MCP Server Integration
+
+Images MUST support dynamic MCP server discovery and configuration through:
+
+1. Environment variable parsing for server count and details
+2. Automatic tool configuration updates
+3. Standard MCP communication protocols
+
+### Persistent Configuration
+
+Images MUST support:
+
+1. Configuration persistence through volume mounts
+2. Symlink creation for tool configuration directories
+3. Proper ownership and permission handling
+
+## Docker Integration
+
+### Dockerfile Requirements
+
+```dockerfile
+# Copy shared scripts from main Cubbi repository
+COPY cubbi_init.py /cubbi_init.py                    # Shared
+COPY init-status.sh /init-status.sh                  # Shared
+
+# Copy tool-specific files
+COPY {tool}_plugin.py /{tool}_plugin.py              # Tool-specific
+COPY cubbi_image.yaml /cubbi/cubbi_image.yaml        # Tool-specific
+
+# Install Python dependencies
+RUN pip install ruamel.yaml
+
+# Make scripts executable
+RUN chmod +x /cubbi_init.py /init-status.sh
+
+# Set entrypoint
+ENTRYPOINT ["/cubbi_init.py"]
+CMD ["tail", "-f", "/dev/null"]
+```
+
+### Init Container Support
+
+For complex initialization, use:
+
+```dockerfile
+# Use init-status.sh as entrypoint for monitoring
+ENTRYPOINT ["/init-status.sh"]
+```
+
+## Best Practices
+
+### Performance
+
+- Use multi-stage builds to minimize image size
+- Clean up package caches and temporary files
+- Use specific base image versions for reproducibility
+
+### Maintainability
+
+- Follow consistent naming conventions
+- Include comprehensive documentation
+- Use semantic versioning for image releases
+- Provide clear error messages and logging
+
+### Compatibility
+
+- Support common development workflows
+- Maintain backward compatibility when possible
+- Test with various project types and configurations
+
+## Validation Checklist
+
+Before releasing a Cubbi image, verify:
+
+- [ ] All required metadata fields are present in `cubbi_image.yaml`
+- [ ] Standard environment variables are supported
+- [ ] `cubbi_init.py` script is properly installed and executable
+- [ ] Tool plugin is discovered and loads correctly
+- [ ] User management works correctly
+- [ ] Persistent configurations are properly handled
+- [ ] MCP integration functions (if applicable)
+- [ ] Tool-specific functionality works as expected
+- [ ] Security requirements are met
+- [ ] Python dependencies are satisfied
+- [ ] Status tracking works correctly
+- [ ] Documentation is complete and accurate
+
+## Examples
+
+### Complete Goose Example
+
+See the `/cubbi/images/goose/` directory for a complete implementation including:
+- `Dockerfile` - Container definition
+- `cubbi_image.yaml` - Image metadata
+- `goose_plugin.py` - Tool-specific initialization
+- `README.md` - Tool-specific documentation
+
+### Migration Notes
+
+The current Python-based system uses:
+- `cubbi_init.py` - Standalone initialization script with plugin support
+- `{tool}_plugin.py` - Tool-specific configuration and MCP integration
+- `init-status.sh` - Status monitoring and log display
+- `cubbi_image.yaml` - Image metadata and configuration